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Sometime in the late 1990s, a vigilante began clearing up Gotham City, which including a corrupted Police Department. Gordon, who was Commissioner at the time, formed an initially uneasy alliance and before long, subsequent friendship with "The Batman". Gordon created the Bat-Signal as a means to contact the enigmatic Batman.

While usually quite serious and practical, Gordon also has a somewhat dry sense of humor, remarking that it was good to see Batman "playing well with others again", upon meeting the Justice League's roster.